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keller_and_evans_lab:gscan [2016/09/12 14:57] scott /* Phenotype definitions and analysis plan */ |
keller_and_evans_lab:gscan [2017/02/14 07:52] scott /* GSCAN GWAS */ |
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======= GSCAN GWAS ======= | ======= GSCAN GWAS ======= | ||
+ | |||
+ | |||
+ | ====== Workgroups ====== | ||
+ | |||
+ | * Phenotype workgroup: Laura Bierut, Marilyn Cornelis, Dave Hinds, Youna Hu, Jaakko Kaprio, Eric Jorgenson, Dajiang Liu, Matt McGue, Marcus Munafo, Gunter Schumann, Scott Vrieze, Luisa Zuccolo | ||
+ | * Analysis workgroup: Goncalo Abecasis, David Hinds, Youna Hu, Eric Jorgenson, Charles Kooperberg, Pete Kraft, Penelope Lind, Dajiang Liu, Nancy Saccone, Dan Stram, Scott Vrieze, Xiaowei Zhan | ||
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- | ====== [[gscan_db_ga_p]] ====== | + | ====== [[gscan_db_ga_p]] |
Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | ||
- | ====== GSCAN use of UKBiobank | + | ======= GSCAN Sequencing ======= |
- | More information about the files used for [[uk_biobank|UKBiobank are here]]. In brief, we used the UK10K + 1kgp3 imputed vcfs provided by UKBionank and added in dosages w/ this python script: | ||
- | import gzip, argparse, re, os, datetime | + | ====== TOPMed ====== |
- | from subprocess import Popen, PIPE | + | |
- | def add_dosage(pair): | + | We hope to update this section with detailed descriptions of how we have conducted phenotype derivations for each TOPMed cohort to which we have access to raw data. |
- | a, b = pair | + | |
- | probs = b.split(b',' | + | |
- | dose = float(probs[1]) + (float(probs[2]) * 2) | + | |
- | return a + b':' | + | |
- | def gziplines(fname): | + | * For now, the R scripts to go from source phenotype file to eventual derived phenotype is located here: |
- | f = Popen([' | + | |
- | | + | |
- | yield line | + | |
- | parser = argparse.ArgumentParser() | + | * We're tracking analyses in [[https:// |
- | parser.add_argument(' | + | |
- | args = parser.parse_args() | + | |
- | flag = False | ||
- | for line in gziplines(args.inputVCF): | + | ===== Phenotype definitions and analysis plan for external studies |
- | if line.startswith(b'#' | + | |
- | os.write(1, line.rstrip() + b' | + | |
- | if not flag: | + | |
- | os.write(1, b'## | + | |
- | os.write(1, b'## | + | |
- | str(datetime.datetime.now()).encode(' | + | |
- | flag = True | + | |
- | else: | + | |
- | elements | + | |
- | first8 | + | |
- | genotypes | + | |
- | form = b' | + | |
- | genotypes_split = zip(genotypes[:: | + | Phenotype definitions and analysis plans for the TOPMed studies are {{file_topmed_smoking_analysis_plan-v0_2.docxcontained |
- | try: | + | |
- | dose_genos = [add_dosage(pair) | + | |
- | except (ValueError, | + | |
- | os.write(2, " | + | |
- | os.write(2, line + " | + | |
- | raise e | + | |
- | os.write(1, b' | + | |
+ | The list of dbGaP studies in TOPMed is in [[https:// | ||
- | ======= | + | ======= |
- | ====== TOPMed ====== | + | While authorship is decided on an individual basis for each GSCAN paper, typically, authorship is arranged in groups. We hope the GIANT investigators will forgive us for adopting their authorship guidelines. |
- | + | * A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, | |
- | ===== Phenotype definitions and analysis plan ===== | + | |
- | + | | |
- | Phenotype definitions | + | |
- | + | | |
- | The list of dbGaP studies | + | * In alphabetical order, senior investigators who participated strongly in GSCAN activities but did not strongly lead/oversee the writing and/or analysis for the paper. Typically, these might be leaders of key GSCAN activities. |
+ | * The senior investigators who strongly led/oversaw the writing and/or analysis of the paper, including a subset that are co-corresponding authors (usually 6 or fewer). | ||